[refine] add 'date_inferred' boolean to output

This is only exported when using `--timetree` and is intended to be
used by `augur export` to inform Auspice whether a date is inferred or
not. An alternative approach would be for `augur export` to parse the
already exported `raw_date` and decide whether that includes ambiguity
but with the proposed changes in <#1304>
this approach is cleaner and less error-prone.

Note that `raw_date_constraint` is None on internal nodes and a list
(of len 2) on terminal nodes with ambiguous dates.

augur/refine.py

@@ -346,7 +346,11 @@ def run(args):
                 )
                 return 1
 
-        attributes.extend(['numdate', 'clock_length', 'mutation_length', 'raw_date', 'date'])
+        for node in T.find_clades():
+            inferred = node.raw_date_constraint is None or isinstance(node.raw_date_constraint, list)
+            setattr(node, 'date_inferred', inferred)
+
+        attributes.extend(['numdate', 'clock_length', 'mutation_length', 'raw_date', 'date', 'date_inferred'])
         if args.date_confidence:
             attributes.append('num_date_confidence')
     else: